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Polymorphism and infection

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https://www.readbyqxmd.com/read/27904617/the-interferon-lambda-4-rs368234815-predicts-treatment-response-to-pegylated-interferon-alpha-and-ribavirin-in-hemophilic-patients-with-chronic-hepatitis-c
#1
Maryam Keshvari, Seyed Moayed Alavian, Bita Behnava, Ali Pouryasin, Heidar Sharafi
BACKGROUND: A dinucleotide variant rs368234815 in interferon lambda 4 (IFNL4) gene was recently found to be associated with the hepatitis C virus (HCV) treatment response. This study aimed to assess the impact of IFNL4 rs368234815 polymorphism on treatment response to pegylated-IFN alpha (Peg-IFN-α) and ribavirin (RBV) in hemophilic patients with chronic hepatitis C (CHC). MATERIALS AND METHODS: In this retrospective study, 92 hemophilic patients with CHC who were treated with Peg-IFN-α/RBV were investigated...
2016: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
https://www.readbyqxmd.com/read/27903797/accumulation-of-pol-mutations-selected-by-hla-b-52-01-c-12-02-protective-haplotype-restricted-ctls-causes-low-plasma-viral-load-due-to-low-viral-fitness-of-mutant-viruses
#2
Hayato Murakoshi, Madoka Koyanagi, Takayuki Chikata, Mohammad Arif Rahman, Nozomi Kuse, Keiko Sakai, Hiroyuki Gatanaga, Shinichi Oka, Masafumi Takiguchi
: HLA-B*52:01-C*12:02, which is the most abundant haplotype in Japan, has a protective effect on disease progression in HIV-1-infected Japanese individuals, whereas HLA-B*57 and -B*27 protective alleles are very rare in Japan. A previous study on HLA-associated polymorphisms demonstrated that the number of HLA-B*52:01-associated mutations at four Pol positions was inversely correlated with plasma viral load (pVL) in HLA-B*52:01-negative individuals, suggesting that the transmission of HIV-1 with these mutations could modulate the pVL in the population...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27902903/characterization-of-thai-mycoplasma-synoviae-isolates-by-sequence-analysis-of-partial-vlha-gene
#3
Kriengwich Limpavithayakul, Jiroj Sasipreeyajan, Somsak Pakpinyo
Mycoplasma synoviae (MS), a remarkable pathogen in poultry, causes subclinical infection of the upper respiratory tract and an infectious synovitis, especially in the tendon sheaths and synovial membranes of joints. Because the specific detection of MS 16S rRNA gene-based PCR was unsuitable for strain differentiation, vlhA gene-based PCR was designed to differentiate the MS strains. The vlhA gene of MS encodes for hemagglutinin and other immunodominant membrane proteins involved in colonization, antigenic variations, and virulence...
December 2016: Avian Diseases
https://www.readbyqxmd.com/read/27902416/the-xylella-fastidiosa-codiro-strain-associated-with-the-olive-quick-decline-syndrome-in-southern-italy-belongs-to-a-clonal-complex-of-the-subspecies-pauca-that-evolved-in-central-america
#4
Marco Scortichini, Simone Marcelletti
Xylella fastidiosa, a xylem-limited bacterium transmitted by xylem-fluid feeding Hemiptera insects, causes economic losses of both woody and herbaceous plant species. A X. fastidiosa subsp. pauca strain, namely CoDiRO, was recently found to be associated with the "olive quick decline syndrome" in southern Italy (i.e., Apulia region). Recently, some X. fastidiosa strains intercepted in France from Coffea spp. plant cuttings imported from Central and South America were characterized. The introduction of infected plant material from Central America in Apulia was also postulated even though an ad hoc study to confirm this hypothesis is lacking...
November 2, 2016: Microbiology
https://www.readbyqxmd.com/read/27902312/genetic-mutations-in-live-infectious-bronchitis-vaccine-viruses-following-single-or-dual-in-vitro-infection-of-tracheal-organ-cultures
#5
Christopher Ball, Sarah Bennett, Anne Forrester, Kannan Ganapathy
Despite regular co-vaccination of two different strains of live infectious bronchitis vaccine viruses, little is known about possible mutations in these viruses following vaccination. As an alternative to chicks, this study used an in-vitro infection model to identify single nucleotide polymorphisms (SNPs) within the part-S1 gene of two live IBV vaccine strains (793B and Massachusetts) following single or dual inoculation onto tracheal organ cultures (TOCs). Results indicate that viral titres reduced over the duration of the study, conversely the amount of detected IBV genome increased...
October 12, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901448/phylogeny-and-haplotype-analysis-of-fungi-within-the-fusarium-incarnatum-equiseti-species-complex
#6
H Ramdial, R K Latchoo, F N Hosein, S N Rampersad
Fusarium spp. are ranked among the top 10 most economically and scientifically important plant-pathogenic fungi in the world and are associated with plant diseases that include fruit decay of a number of crops. Fusarium isolates infecting bell pepper in Trinidad were identified based on sequence comparisons of the translation elongation factor gene (EF-1a) with sequences of Fusarium incarnatum-equiseti species complex (FIESC) verified in the FUSARIUM-ID database. Eighty-two isolates were identified as belonging to one of four phylogenetic species within the subclades FIESC-1, FIESC-15, FIESC-16, and FIESC-26, with the majority of isolates belonging to FIESC-15...
November 30, 2016: Phytopathology
https://www.readbyqxmd.com/read/27901085/wide-variation-in-susceptibility-of-transmitted-founder-hiv-1-subtype-c-isolates-to-protease-inhibitors-and-association-with-in-vitro-replication-efficiency
#7
Katherine A Sutherland, Dami A Collier, Daniel T Claiborne, Jessica L Prince, Martin J Deymier, Richard A Goldstein, Eric Hunter, Ravindra K Gupta
The gag gene is highly polymorphic across HIV-1 subtypes and contributes to susceptibility to protease inhibitors (PI), a critical class of antiretrovirals that will be used in up to 2 million individuals as second-line therapy in sub Saharan Africa by 2020. Given subtype C represents around half of all HIV-1 infections globally, we examined PI susceptibility in subtype C viruses from treatment-naïve individuals. PI susceptibility was measured in a single round infection assay of full-length, replication competent MJ4/gag chimeric viruses, encoding the gag gene and 142 nucleotides of pro derived from viruses in 20 patients in the Zambia-Emory HIV Research Project acute infection cohort...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899155/comparative-sequence-analysis-of-cyclospora-cayetanensis-apicoplast-genomes-originating-from-diverse-geographical-regions
#8
Hediye Nese Cinar, Yvonne Qvarnstrom, Yuping Wei-Pridgeon, Wen Li, Fernanda S Nascimento, Michael J Arrowood, Helen R Murphy, AhYoung Jang, Eunje Kim, RaeYoung Kim, Alexandre da Silva, Gopal R Gopinath
BACKGROUND: Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis...
November 29, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27898592/the-hepatitis-c-virus-nonstructural-protein-3-q80k-polymorphism-is-frequently-detected-and-transmitted-among-hiv-infected-msm-in-the-netherlands
#9
Astrid M Newsum, Cynthia K Y Ho, Faydra I Lieveld, Thijs J W van de Laar, Sylvie M Koekkoek, Sjoerd P Rebers, Jan T M van der Meer, Anne M J Wensing, Greet J Boland, Joop E Arends, Karel J van Erpecum, Maria Prins, Richard Molenkamp, Janke Schinkel
OBJECTIVES: The Q80K polymorphism is a naturally occurring resistance-associated variant in the hepatitis C virus (HCV) nonstructural protein 3 (NS3) region and is likely transmissible between hosts. This study describes the Q80K origin and prevalence among HCV risk groups in the Netherlands and examines whether Q80K is linked to specific transmission networks. DESIGN AND METHODS: Stored blood samples from HCV genotype 1a-infected patients were used for PCR and sequencing to reconstruct the NS3 maximum likelihood phylogeny...
January 2, 2017: AIDS
https://www.readbyqxmd.com/read/27898140/ny-subtyp-av-molluscipoxvirus-p%C3%A3-visad-modern-teknik-identifierar-nya-och-ovanliga-patogener-snabbare
#10
Anna-Lena Hammarin, Yvonne Eklund, Maria Karlberg, Morten Bogh, Per Sikora
Molluscum contagiosum is a viral infection of the epidermis characterized by skin-colored papules or nodules frequently with a central depression. Atypical variants may occur, primarily in immunosuppressed individuals. We here report a case of »giant Molluscum contagiosum« in an immunocompetent child. The patient was presented with a fairly smooth nodule of 2 cm in diameter on the ring finger. Molluscipoxvirus-like virus particles were detected by electron microscopy from the nodule, but since the clinical picture was not compatible with MC, next generation sequencing was performed in order to verify the diagnosis...
November 28, 2016: Läkartidningen
https://www.readbyqxmd.com/read/27896747/studying-antibody-repertoires-with-next-generation-sequencing
#11
William D Lees, Adrian J Shepherd
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896690/elucidating-the-plasma-and-liver-pharmacokinetics-of-simeprevir-in-special-populations-using-physiologically-based-pharmacokinetic-modelling
#12
Jan Snoeys, Maria Beumont, Mario Monshouwer, Sivi Ouwerkerk-Mahadevan
The disposition of simeprevir (SMV) in humans is characterised by cytochrome P450 3A4 metabolism and hepatic uptake by organic anion transporting polypeptide 1B1/3 (OATP1B1/3). This study was designed to investigate SMV plasma and liver exposure upon oral administration in subjects infected with hepatitis C virus (HCV), in subjects of Japanese or Chinese origin, subjects with organ impairment and subjects with OATP genetic polymorphisms, using physiologically based pharmacokinetic modelling. Simulations showed that compared with healthy Caucasian subjects, SMV plasma exposure was 2...
November 29, 2016: Clinical Pharmacokinetics
https://www.readbyqxmd.com/read/27895405/impact-of-il28b-and-oas-gene-family-polymorphisms-on-interferon-treatment-response-in-caucasian-children-chronically-infected-with-hepatitis-b-virus
#13
Krzysztof Domagalski, Małgorzata Pawłowska, Agnieszka Zaleśna, Małgorzata Pilarczyk, Paweł Rajewski, Waldemar Halota, Andrzej Tretyn
AIM: To investigate the impact of IL28B and OAS gene polymorphisms on interferon treatment responses in children with chronic hepatitis B. METHODS: We enrolled 52 children (between the ages of 4 and 18) with hepatitis B e antigen-negative chronic hepatitis B (CHB), who were treated with pegylated interferon alfa for 48 wk. Single nucleotide polymorphisms in the OAS1 (rs1131476), OAS2 (rs1293747), OAS3 (rs2072136), OASL (rs10849829) and IL28B (rs12979860, rs12980275 and rs8099917) genes were studied to examine their associations with responses to IFN treatment in paediatric patients...
November 7, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27894112/association-of-mbl2-gene-polymorphism-with-dental-caries-in-saudi-children
#14
Yousef M Alyousef, J Francis Borgio, Sayed AbdulAzeez, Naif Al-Masoud, Ali A Al-Ali, Emad Al-Shwaimi, Amein K Al-Ali
The high prevalence of dental caries in children worldwide is a major oral health problem which requires early intervention. Dental caries is mainly caused by the action of acids produced by bacteria in addition to many other factors. Recent genetic studies have reported that a number of genes are associated with the susceptibility to dental caries. The majority of these genes are associated with inflammation, increased susceptibility to infection, and dentine matrix formation. Using the TaqMan assay and direct DNA sequencing, the prevalence of 6 single-nucleotide polymorphisms (SNPs) in MMP9, MBL2, MMP2, and TIMP2 genes was determined in 102 children with caries and in 100 age-matched caries-free controls...
November 29, 2016: Caries Research
https://www.readbyqxmd.com/read/27894089/associations-between-single-nucleotide-polymorphisms-of-human-exonuclease-1-and-the-risk-of-hepatocellular-carcinoma
#15
Shengkui Tan, Ruoyun Qin, Xiaonian Zhu, Chao Tan, Jiale Song, Linyuan Qin, Liu Liu, Xiong Huang, Anhua Li, Xiaoqiang Qiu
Human exonuclease 1 (hEXO1) is an important nuclease involved in mismatch repair system that contributes to maintain genomic stability and modulate DNA recombination. This study is aimed to explore the associations between single-nucleotide polymorphisms (SNPs) of hEXO1 and the hereditary susceptibility of hepatocellular carcinoma (HCC). SNPs rs1047840, rs1776148, rs3754093, rs4149867, rs4149963, and rs1776181 of hEXO1 were examined from a hospital-based case-control study including 1,196 cases (HCC patients) and 1,199 controls (non-HCC patients) in Guangxi, China...
November 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27892677/ccr5-polymorphism-as-a-protective-factor-for-hepatocellular-carcinoma-in-hepatitis-b-virus-infected-iranian-patients
#16
Abdolmohammadi Reza, Shahbazi Azar Saleh, Khosravi Ayyoob, Shahbazi Majid
The CC chemokine receptor 5 (CCR5) delta 32 allele results in a nonfunctional form of the chemokine receptor and has been implicated in a variety of immune-mediated diseases. CCR5Δ32 may also predispose one to chronic liver disease or be linked with resistance to HBV infection.This study was undertaken to investigate any association between CCR5 polymorphism with resistance to hepatitis B or susceptibility to HBV infection. A total of 812 Iranian individuals were enrolled into two groups: HBV infected cases (n=357), who were HBsAg-positive, and healthy controls (n=455)...
January 10, 2016: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/27891480/traumatic-ulcerative-granuloma-with-stromal-eosinophila-a-case-report-and-review-of-pathogenesis
#17
Bhushan Sharma, George Koshy, Shekhar Kapoor
Traumatic Ulcerative Granuloma with Stromal Eosinophilia (TUGSE) is an uncommon condition considered to be a, reactive benign lesion of the oral mucosa, usually affecting the tongue. Its aetiopathogenesis is still uncertain. However, trauma has been found to be a contributing factor in a majority of the cases. Clinically, it often presents as an isolated ulcer or an indurated submucosal mass. Microscopically, it is characterized by a diffuse polymorphic cell infiltrate composed predominantly of eosinophils, B and T lymphocytes, macrophages, and large atypical cells involving the superficial mucosa and extending deep into the submucosa causing degeneration of the underlying muscle...
October 2016: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/27890033/il-8-il-17-gene-variations-and-the-susceptibility-to-severe-viral-bronchiolitis
#18
L A Pinto, L A DE Azeredo Leitão, M Mocellin, P Acosta, M T Caballero, R Libster, J E Vargas, F Polack, T Comaru, R T Stein, A P DE Souza
Clinical manifestations of acute bronchiolitis (AB) vary from minimal disease to severe respiratory failure. The response to respiratory viral infections is possibly influenced by genetic polymorphisms linked to the regulation of the inflammatory response. In the present study, we investigated whether interleukin-8 (IL-8) and interleukin-17 (IL-17) genetic variants are associated with the severity of AB. A group of Brazilian infants hospitalized with AB and a control group (infants with no or mild AB, without hospitalization) were genotyped for four IL-8/IL-17 variations...
November 28, 2016: Epidemiology and Infection
https://www.readbyqxmd.com/read/27889163/differential-detection-of-pathogenic-yersinia-spp-by-fluorescence-in-situ-hybridization
#19
Alexander Rohde, Jens Andre Hammerl, Bernd Appel, Ralf Dieckmann, Sascha Al Dahouk
Yersinia enterocolitica, Y. pseudotuberculosis and Y. pestis are pathogens of major medical importance, which are responsible for a considerable number of infections every year. The detection of these species still relies on cultural methods, which are slow, labour intensive and often hampered by the presence of high amounts of accompanying flora. In this study, fluorescence in situ hybridization (FISH) was used to develop a fast, sensitive and reliable alternative to detect viable bacteria in food. For this purpose, highly specific probes targeting the 16S and 23S ribosomal RNA were employed to differentially detect each of the three species...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27888301/the-genome-sequence-and-insights-into-the-immunogenetics-of-the-bananaquit-passeriformes-coereba-flaveola
#20
Jennifer Antonides, Robert Ricklefs, J Andrew DeWoody
Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome...
November 25, 2016: Immunogenetics
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